/ 
BioPerl-1.7.8
River stage two • 61 direct dependents • 66 total dependents
/ Bio::Tools::TandemRepeatsFinder

NAME

Bio::Tools::TandemRepeatsFinder - a parser for Tandem Repeats Finder output

SYNOPSIS

use Bio::Tools::TandemRepeatsFinder;

# create parser
my $parser = Bio::Tools::Bio::Tools::TandemRepeatsFinder->new(-file => 'tandem_repeats.out');

# loop through results
while( my $feature = $parser->next_result ) {

    # print the source sequence id, start, end, percent matches, and the consensus sequence
    my ($percent_matches)    = $feat->get_tag_values('percent_matches');
    my ($consensus_sequence) = $feat->get_tag_values('consensus_sequence');
    print $feat->seq_id()."\t".$feat->start()."\t".$feat->end()."\t$percent_matches\t$consensus_sequence\n"; 

}

DESCRIPTION

A parser for Tandem Repeats Finder output. Written and tested for version 4.00

Location, seq_id, and score are stored in Bio::SeqFeature::Generic feature. All other data is stored in tags. The available tags are

period_size
copy_number
consensus_size
percent_matches
percent_indels
percent_a
percent_c
percent_g
percent_t
entropy
consensus_sequence
repeat_sequence
run_parameters
sequence_description

The run_parameters are stored in a hashref with the following key:

match_weight
mismatch_weight
indel_weight
match_prob
indel_prob
min_score
max_period_size

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Eric Just

Email e-just@northwestern.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $obj = Bio::Tools::TandemRepeatsFinder->new();
Function: Builds a new Bio::Tools::TandemRepeatsFinder object
Returns : Bio::Tools::TandemRepeatsFinder
Args    : -fh/-file => $val, for initing input, see Bio::Root::IO

version

Title   : version
Usage   : $self->version( $version )
Function: get/set the version of Tandem Repeats finder that was used in analysis
Returns : value of version of 
Args    : new value (optional)

_current_seq_id

Title   : _current_seq_id
Usage   : $self->_current_seq_id( $current_seq_id )
Function: get/set the _current_seq_id
Returns : value of _current_seq_id
Args    : new value (optional)

_current_seq_description

Title   : _current_seq_description
Usage   : $self->_current_seq_description( $current_seq_id )
Function: get/set the _current_seq_description
Returns : value of _current_seq_description
Args    : new value (optional)

_current_parameters

Title   : _current_parameters
Usage   : $self->_current_parameters( $parameters_hashref )
Function: get/set the _current_parameters
Returns : hashref representing current parameters parsed from results file
        : keys are
              match_weight
              mismatch_weight
              indel_weight
              match_prob
              indel_prob
              min_score
              max_period_size
Args    : parameters hashref (optional)

next_result

Title   : next_result
Usage   : my $r = $trf->next_result()
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args    : none

_create_feature

Title   : _create_feature
Usage   : internal method used by 'next_feature'
Function: Takes a line from the results file and creates a bioperl object
Returns : Bio::SeqFeature::Generic
Args    : none